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karyotapR: DNA Copy Number Analysis for Genome-Wide Tapestri Panels
Analysis of DNA copy number in single cells using
custom genome-wide targeted DNA sequencing panels for the Mission Bio
Tapestri platform. Users can easily parse, manipulate, and visualize
datasets produced from the automated 'Tapestri Pipeline', with support for
normalization, clustering, and copy number calling. Functions are also
available to deconvolute multiplexed samples by genotype and parsing
barcoded reads from exogenous lentiviral constructs.
| Version: |
1.0.1 |
| Depends: |
R (≥ 3.6), SingleCellExperiment |
| Imports: |
circlize, cli, ComplexHeatmap, dbscan, dplyr, fitdistrplus, GenomicRanges, ggplot2, gtools, IRanges, magrittr, methods, purrr, rhdf5, rlang, S4Vectors, stats, SummarizedExperiment, tibble, tidyr, umap, viridisLite |
| Suggests: |
Biostrings, knitr, rmarkdown, Rsamtools, testthat (≥ 3.0.0) |
| Published: |
2023-09-07 |
| DOI: |
10.32614/CRAN.package.karyotapR |
| Author: |
Joseph Mays  [aut,
cre, cph] |
| Maintainer: |
Joseph Mays <josephcmays at gmail.com> |
| BugReports: |
https://github.com/joeymays/karyotapR/issues |
| License: |
MIT + file LICENSE |
| URL: |
https://github.com/joeymays/karyotapR,
http://joeymays.xyz/karyotapR/ |
| NeedsCompilation: |
no |
| Materials: |
README NEWS |
| CRAN checks: |
karyotapR results |
Documentation:
Downloads:
Linking:
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https://CRAN.R-project.org/package=karyotapR
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These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.